Multi-omic landscape of squamous cell lung cancer

We identified 116 patients consented to the Total Cancer Care (TM) protocol that had donated snap frozen lung squamous cell carcinoma tumor tissues with linked molecular data as well as clinical history, tumor pathology, and patient outcomes. Samples were collected under the Moffitt's Total Cancer Care protocol (Liberty IRB # 12.11.0023) and Moffitt's General Banking protocol (IRB #: USF 101642). Described experiments were considered non-human subjects research and performed under protocol MCC #50083. Overall design: Qiagen's AllPrep DNA/RNA Mini kit was used for the simultaneous purification of genomic DNA and total RNA from the homogenized tumor tissue aliquot. RNAseq was performed using the NuGen Ovation Encore Complete RNAseq kit, which generates strand-specific total RNAseq libraries (Nugen, Inc., San Carlos, CA). A custom Agilent SureSelect panel covering 154 total genes (151 genes from the ClearSeq Comprehensive Cancer Panel plus KMT2D, KEAP1, and NFE2L2) was designed and used for the enrichment of DNA libraries generated using the Agilent SureSelect XT Library Kit (Agilent Technologies, Santa Clara, CA).